Aircraft: CHALLENGER 350
Phase of flight: Parked
Anomaly: Deviation / Discrepancy - Procedural Security; Deviation / Discrepancy - Procedural Published Material / Policy; Flight Deck / Cabin / Aircraft Event Other / Unknown

I was the assigned First Officer to Aircraft X. On the evening [prior to departure]; I requested a cleaning of the aircraft. Prior to the cleaning; the aircraft was secured per the FOM which included; but not limited to; disconnecting the batteries and locking the battery door; pinning the emergency exit (a red flag hangs down inside the cabin while the pin is in identifying it); and a security seal was applied.Upon showing to the aircraft [the next day] for a hot spare duty assignment; we first noticed the battery door was unlocked and the two batteries were connected. While unusual; it's not completely unheard of for this. Usually means that maintenance was on the aircraft and were either still working on it or forgot to secure it.The door was sealed with a maintenance seal. The seal was placed there by the cleaners we later found out.When we opened the door; we looked in the rear cabin and noticed that the emergency exit flag was gone and the cover was in place. From all appearances; the pin was removed from the airplane. This raised our suspicion level and we continued our preflight/investigation of the interior.When I inspected the flight deck; I noticed that my seat belt was straightened and not how I left it. This was due to the cleaners. When I started applying power to the airplane; I noticed that a rubber button on the right side FMS was broken. Button L1. Something heavy must have scraped up against it because while the button was literally hanging by a thread; the plastic tab between the button and the device sensor was located about 3 feet away on the center console.At this point; I went and located our contract maintenance on field and asked if anyone from them was on the aircraft. They said no. I located the cleaning company and discussed the situation with the supervisor. He said that the battery was already hooked up when they got there and that they didn't touch the pin and flag. Based on this information; we decided that at some point the chain of custody was lost and we contacted [Company] security for further guidance. We were told to contact local police for assistance. We gave a statement to the officer; and we requested a bomb sniffing dog to inspect the aircraft. One arrived several hours later and swept the aircraft. No devices were found. Furthermore; when we were showing the emergency exit pin placement to the officer; we took the cover off and found the exit was indeed pinned but the flag was folded up and the cover replaced.Since this occurred at night; we requested additional time the next day to do a visual sweep of the airplane. We got the ladders out and inspected the APU exhaust and other normally inaccessible places.We had a passenger flight [that day]. This was the first flight since the security incident. While enroute; I noticed on the audio control panel that the 'emergency' switch was broken; and the two switches next to it were bent. I had missed this on the preflight; and this is an Aircraft on Ground item. The damage indicated that someone had either hit it with something heavy or kicked it when they were getting into or out of the cockpit chair.The aircraft was grounded [at destination airport] affecting further flights.Based on the evidence at hand; I believe the following events happened:The cleaners thought that since the panel was off of the emergency exit; they put it back thinking they were doing the right thing by folding up the flag.The cleaners connected the battery to raise the door using the motor assist and left it connected.The cleaners damaged the cockpit while cleaning it. The cleaner likely swiped his foot across the FMS panel while getting in or out; and also kicked the audio control panel damaging the three switches.The audio control panel is part of my normal preflight duties. I should have caught the damage prior to the flight. I take full responsibility for this omission.I think that the cleaners need to be told NOT to touch the batteries; any flags; and to stay out of the cockpit. Challenger 350 First Officer reported that there was evidence that the airplane may have been tampered with while sitting on the ramp all night.